Transcriptome analysis

presentation

1. Transcriptome analysis Submitted by:-Rama Jumwal M.sc. (biotechnology) MAU20PBT010

2. Transcriptome A transcriptome is the set of all RNA molecules including mRNA,rRNA,tRNA and other non coding RNAs(ncRNAs) produced in a population of cells The term can be applied to the total set of transcripts in a given organism,or to the specific subset of transcripts present in a particular cell type under specific conditions The transcriptome can vary in different parts of the body and may also differ with external environment conditions

3. Positional information integration on transcriptome

4. Transcriptomics Transcriptomics Is the study of rna in any of its forms A study of transcriptome elucidates the complex interactions which generally take place among the transcripts before these are translated Also an independent analysis of transcriptome in thousand of cell types ,organs and tissues elucidates regulation of gene expression in time and space through the study of relative abundance of different individual transcripts

5. Transcriptomics aims To catalogue all species of transcripts,including mRNAs,non codingRNAs and small RNAs To determine the transcriptional structure of genes in terms of their start sites,5’and 3’ ends, and other post transcriptional modifications To quantify the changing expression levels of each transcript during development and under different conditions

6. Methods There are two main transcriptomics techniques include DNA microarrays RNA sequencing

7. Microarrays “two colour ” or cDNA or two channel microarrays “One colour or oligonucleotides or one channel microarrays

8. One channel microarray One channel microarrays are based on RNA of one sample which has been labeled with a fluorescent dye and hybridized to a single array where millions of copies of short oligonucleotide probes representing all known genes have been synthesized After exposition to laser light and scanner the intensity of each location is measured yielding a value which represents an absolute measure of expression

9. Two colour microarrays Two colour microarrays are based on competitive hybridisation of two samples each of which has been labelled with a different fluorescent dye e.g.red or green After hybridisation the array is exposed to red and green laser light the array emits fluorescent proportional to quantity of RNA The image produced is scanned yielding after some corrections a value which represents the expression of one sample relative to other

10. RNA -sequencing RNA-sequencing transcriptomics replaces the hybridisation of nucleotides probes with sequencing individual cDNAs produced from target RNA Emerging methods for these fully quantitative transcriptomic analysis have the potential to overcome the limitations of microarray technology and there are ongoing discussions about sequencing approaches ma replace microarrays in the middle or even short term As a massively parallel process next generation sequencing (NGS) generates hundreds of megabites to gigabites of nucleotide sequence output in a single instrument run,depending on the platform

11. NGS technologies Roche 454 Illumina genome analyzer sequencing Applied biosystems solid sequencing

12. References www.slideshre.net/mohamadoseinromena/transcriptomics www.slideshare.net/divyasrivastava17/transcriptomeanalysis https://d2cax41o7ahm5l.cloudfront.net Cell and molecular biology by P.K.gupta fourth revised edison /part 6 chapter-69( genomics,transcriptomics,proteomics and metabolomics )